[gmx-users] High Initial generated Temp

[tarak karmakar]

I'm extremely sorry for copying the other '.mdp' file here. This is the
modified one I just created after seeing your reply. In the previous case I
didn't use 'continuation'.


On Tue, Jun 4, 2013 at 9:47 PM, tarak karmakar <tarak20489 at gmail.com> wrote:

> Thanks Justin.
> Sorry for not uploading the full .mdp. Here it is,
>
> ; 7.3.3 Run Control
> integrator              = md
> tinit                   = 0
> dt                      = 0.001
> nsteps                  = 5000000
> nstcomm                 = 1
> comm_grps               = system
> comm_mode               = linear
> energygrps              = system
>
> ; 7.3.8 Output Control
> nstxout                 = 5000
> nstfout                 = 5000
> nstlog                  = 1000
> nstenergy               = 1000
> nstxtcout               = 1000
> xtc_precision           = 1000
> xtc_grps                = System
>
> ; 7.3.9 Neighbor Searching
> nstlist                 = 10
> ns_type                 = grid
> pbc                     = xyz
> rlist                   = 1.2
> rlistlong               = 1.4
>
> ; 7.3.10 Electrostatics
> coulombtype             = PME
> rcoulomb                = 1.2
> fourierspacing          = 0.12
> pme_order               = 4
> ewald_rtol              = 1e-5
>
> ; 7.3.11 VdW
> vdwtype                 = switch
> rvdw                    = 1.2
> rvdw-switch             = 1.0
>
> DispCorr                = Ener
>
>
> ; 7.3.14 Temperature Coupling
> tcoupl                  = nose-hoover
> tc_grps                 = system
> tau_t                   = 1.0
> ref_t                   = 300
>
> ; 7.3.15 Pressure Coupling
> pcoupl                  = parrinello-rahman
> pcoupltype              = isotropic
> tau_p                   = 1.0
> compressibility         = 4.5e-5
> ref_p                   = 1.0
>
> gen_vel                 = yes
> gen_temp                = 300
> gen_seed                = 93873959697
>
> ; 7.3.18 Bonds
> constraints             = h-bonds
> constraint_algorithm    = LINCS
> continuation            = yes
> lincs_order             = 4
> lincs_iter              = 1
> lincs_warnangle         = 30
>
> Note: Using CHARMM27 force field
>
> I didn't use the 'continuation' part here.
> In the heating run I didn't put any constraints but in the production MD,
> I do apply constraints to the covalent bonds involving hydrogens. I just
> want to test the ligand movement inside the protein cavity in different set
> of initial velocities to get the feelings of how ligand is interacting with
> certain residues.
> So, then should I use these different velocity generating seeds during the
> warm up step?
>
> Thanks,
> Tarak
>
>
>
>
>
>
>
> On Tue, Jun 4, 2013 at 5:46 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 6/4/13 8:07 AM, tarak karmakar wrote:
>>
>>> Dear All,
>>>
>>> Although I have set gen_temp = 300, it is showing the initial temperature
>>> 445.7 K, generated at the very beginning  of the run.
>>>
>>> gen_vel                 = yes             ; velocity generation
>>> gen_temp                = 300
>>> gen_seed                = 93873959697
>>>
>>> Is it because of a bad geometry? In mailing list I came across this
>>> thread
>>> [ http://comments.gmane.org/**gmane.science.biology.gromacs.**user/41931<http://comments.gmane.org/gmane.science.biology.gromacs.user/41931>
>>> ]
>>> Prior to this production run, I heated my system slowly from 0 K to 300 K
>>> within 300 ps time span.
>>> It would be very helpful if someone suggests me the way to deal with this
>>> problem?
>>>
>>>
>> A full .mdp file is always more useful than a small snippet.  I have seen
>> this same behavior when the "continuation" parameter is incorrectly set -
>> have you used "continuation = yes" in your .mdp file?  If not, the
>> constraints get messed up and your initial velocities can get all messed up.
>>
>> A larger point is this - why are you re-generating velocities after
>> heating the system from 0 to 300 K?  Why not simply preserve the ensemble
>> at 300 K by using a .cpt file?
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>> * Please search the archive at http://www.gromacs.org/**
>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
>> * Please don't post (un)subscribe requests to the list. Use the www
>> interface or send it to gmx-users-request at gromacs.org.
>> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>
>
>
>
>